lederhosen 0.0.3 → 0.0.4

data/lib/lederhosen/tasks/cluster.rb

@@ -0,0 +1,30 @@
+##
+# FINALLY, CLUSTER!
+#
+
+module Lederhosen
+  class CLI
+
+    desc "cluster fasta file",
+         "--input=sorted.fasta --identity=0.80 --output=clusters.uc"
+
+    method_option :input,    :type => :string,  :default => 'sorted.fasta'
+    method_option :output,   :type => :string,  :default => 'clusters.uc'
+    method_option :identity, :type => :numeric, :default => 0.8
+
+    def cluster
+      identity = options[:identity]
+      output = options[:output]
+      input = options[:input]
+    
+      cmd = [
+        'uclust',
+        "--input #{input}",
+        "--uc #{output}",
+        "--id #{identity}",
+      ].join(' ')
+      exec cmd
+    end
+
+  end
+end

data/lib/lederhosen/tasks/join.rb

@@ -0,0 +1,35 @@
+module Lederhosen
+  class CLI
+
+    ##
+    # PAIRED-END READ WORK-AROUND (JOIN THEM)
+    #
+    desc "join reads end-to-end",
+         "--trimmed=trimmed/*.fasta --output=joined.fasta"
+
+    method_option :trimmed, :type => :string, :default => 'trimmed/*,fasta'
+    method_option :output,  :type => :string, :default => 'joined.fasta'
+
+    def join
+
+      trimmed = Dir[options[:trimmed]]
+      output = options[:output]
+
+      fail "no reads in #{trimmed}" if trimmed.length == 0
+
+      output = File.open(output, 'w')
+
+      pbar = ProgressBar.new "joining", trimmed.length
+
+      trimmed.each do |fasta_file|
+        pbar.inc
+        records = Dna.new File.open(fasta_file)
+        records.each_slice(2) do |r, l|
+          output.puts ">#{r.name}:#{File.basename(fasta_file, '.fasta')}\n#{r.sequence.reverse+l.sequence}"
+        end
+      end
+      pbar.finish
+    end
+
+  end
+end

data/lib/lederhosen/tasks/otu_table.rb

@@ -0,0 +1,61 @@
+##
+# MAKE TABLES
+#
+
+module Lederhosen
+  class CLI
+
+    desc "otu_tables generates otu tables & representative reads",
+         "--clusters=clusters.uc --output=otu_prefix --joined=joined.fasta"
+
+    method_option :clusters, :type => :string, :default => 'clusters.uc'
+    method_option :output,   :type => :string, :default => 'otus'
+    method_option :joined,   :type => :string, :default => 'joined.fasta'
+
+    def otu_table
+      input = options[:clusters]
+      output = options[:output]
+      joined_reads = options[:joined]
+
+      clusters = Hash.new
+
+      # Load cluster table!
+      clusters = Helpers.load_uc_file(input)
+
+      clusters_total = clusters[:count_data].values.collect{ |x| x[:total] }.inject(:+)
+
+      # Get representative sequences!
+      reads_total = 0
+      representatives = {}
+      clusters[:count_data].each{ |k, x| representatives[x[:seed]] = k }
+
+      out_handle = File.open("#{output}.fasta", 'w')
+
+      File.open(joined_reads) do |handle|
+        records = Dna.new handle
+        records.each do |dna|
+          reads_total += 1
+          if !representatives[dna.name].nil?
+            dna.name = "#{dna.name}:cluster_#{representatives[dna.name]}"
+            out_handle.puts dna
+          end
+        end
+      end
+
+      out_handle.close
+
+      # Print some statistics
+      ohai "reads in clusters:  #{clusters_total}"    
+      ohai "number of reads:    #{reads_total}"
+      ohai "unique clusters:    #{clusters.keys.length}"
+
+      # print OTU abundancy matrix
+      csv = Helpers.cluster_data_as_csv(clusters)
+      File.open("#{output}.csv", 'w') do |h|
+        h.puts csv
+      end
+
+    end
+
+  end
+end

data/lib/lederhosen/tasks/sort.rb

@@ -0,0 +1,22 @@
+##
+# SORT JOINED READS BY LENGTH
+#
+
+module Lederhosen
+  class CLI
+
+    desc "sort fasta file by length",
+         "--input=joined.fasta --output=sorted.fasta"
+
+    method_options :input => :string, :output => :string
+    method_option :input,  :type => :string, :default => 'joined.fasta'
+    method_option :output, :type => :string, :default => 'sorted.fasta'
+
+    def sort
+      input = options[:input]
+      output = options[:output]
+      `uclust --mergesort #{input} --output #{output}`
+    end
+
+  end
+end

data/lib/lederhosen/tasks/split.rb

@@ -0,0 +1,81 @@
+##
+# Create a fasta file with nucleotide sequences for each cluster larger than a cutoff
+#
+
+module Lederhosen
+  class CLI
+
+    desc "output separate fasta file containing sequences belonging to each cluster",
+         "--clusters=clusters.uc --reads=joined.fasta --min-clst-size=100"
+
+    method_option :clusters,      :type => :string,  :default => 'clusters.uc'
+    method_option :reads,         :type => :string,  :default => 'joined.fasta'
+    method_option :out_dir,       :type => :string,  :default => 'clusters_split'
+    method_option :buffer_size,   :type => :numeric, :default => 1000
+    method_option :min_clst_size, :type => :numeric, :default => 100
+
+    def split
+      clusters = options[:clusters]
+      reads    = options[:reads]
+      out_dir  = options[:out_dir]
+      buffer_size = options[:buffer_size]
+      min_clst_size = options[:min_clst_size]
+      finalize_every = 100_000
+
+      `mkdir -p #{out_dir}/`
+
+      ohai "loading #{clusters}"
+
+      # Load read id -> cluster
+      read_to_clusterid = Hash.new
+
+      # keep track of cluster sizes
+      cluster_counts    = Hash.new { |h, k| h[k] = 0}
+
+      File.open(clusters)do |handle|
+        handle.each do |line|
+          line = line.strip.split
+          cluster_nr = line[1]
+          if line[0] == 'S' || line[0] == 'H'
+            read = line[8]
+          else
+            next
+          end
+          read_to_clusterid[read] = cluster_nr
+          cluster_counts[cluster_nr] += 1
+        end
+      end
+
+      read_to_clusterid.delete_if do |read, cluster_nr|
+        cluster_counts[cluster_nr] < min_clst_size
+      end
+
+      total_reads = read_to_clusterid.length
+      total_clusters = read_to_clusterid.values.uniq.length
+      ohai "#{total_reads} reads in #{total_clusters} clusters"
+
+      pbar = ProgressBar.new "saving", total_reads
+
+      # Write reads to individual fasta files using Buffer
+      buffer = Buffer.new :buffer_max => buffer_size
+      File.open(reads) do |handle|
+        records = Dna.new handle
+        records.each_with_index do |record, i|
+          cluster_id = read_to_clusterid[record.name]
+          if cluster_id
+            pbar.inc
+            filename = File.join(out_dir, cluster_id + '.fasta')
+            buffer[filename] << record
+            buffer.finalize if (i%finalize_every == 0)
+          end
+        end
+      end
+
+      pbar.finish
+      ohai "finalizing output"
+      buffer.finalize # finish writing out
+
+      puts "done"
+    end
+  end
+end

data/lib/lederhosen/tasks/trim.rb

@@ -0,0 +1,36 @@
+##
+# QUALITY TRIMMING
+#
+
+module Lederhosen
+  class CLI
+
+    desc "trim Illumina QSEQ files",
+         "--reads_dir=reads/* --out_dir=trimmed.fasta"
+
+    method_option :reads_dir, :type => :string, :required => true
+    method_option :out_dir,   :type => :string, :default => 'trimmed/'
+
+    def trim
+
+      raw_reads = options[:reads_dir]
+      out_dir = options[:out_dir]
+
+      `mkdir -p #{out_dir}`
+
+      raw_reads = Helpers.get_grouped_qseq_files raw_reads
+      ohai "found #{raw_reads.length} pairs of reads"
+
+      pbar = ProgressBar.new "trimming", raw_reads.length
+
+      raw_reads.each do |a|
+        pbar.inc
+        out = File.join(out_dir, "#{File.basename(a[0])}.fasta")
+        # TODO get total and trimmed
+        total, trimmed = Helpers.trim_pairs a[1][0], a[1][1], out, :min_length => 70
+      end
+
+      pbar.finish
+    end
+  end
+end

data/lib/version.rb

@@ -1,3 +1,3 @@
 module Lederhosen
-  VERSION = '0.0.3'
+  VERSION = '0.0.4'
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: lederhosen
 version: !ruby/object:Gem::Version 
-  hash: 25
+  hash: 23
   prerelease: 
   segments: 
   - 0
   - 0
-  - 3
-  version: 0.0.3
+  - 4
+  version: 0.0.4
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -120,6 +120,12 @@ files:
 - lib/lederhosen/buffer.rb
 - lib/lederhosen/cli.rb
 - lib/lederhosen/helpers.rb
+- lib/lederhosen/tasks/cluster.rb
+- lib/lederhosen/tasks/join.rb
+- lib/lederhosen/tasks/otu_table.rb
+- lib/lederhosen/tasks/sort.rb
+- lib/lederhosen/tasks/split.rb
+- lib/lederhosen/tasks/trim.rb
 - lib/version.rb
 - readme.md
 - spec/data/ILT_L_9_B_001_1.txt